Single-cell, whole-embryo phenotyping of mammalian developmental disorders

Mouse models are a critical tool for studying human diseases, particularly developmental disorders. However, conventional approaches for phenotyping may fail to detect subtle defects throughout the developing mouse. Here we set out to establish single-cell RNA sequencing of the whole embryo as a scalable platform for the systematic phenotyping of mouse genetic models. We applied combinatorial indexing-based single-cell RNA sequencing to profile 101 embryos of 22 mutant and 4 wild-type genotypes at embryonic day 13.5, altogether profiling more than 1.6 million nuclei. The 22 mutants represent a range of anticipated phenotypic severities, from established multisystem disorders to deletions of individual regulatory regions. We developed and applied several analytical frameworks for detecting differences in composition and/or gene expression across 52 cell types or trajectories. Some mutants exhibit changes in dozens of trajectories whereas others exhibit changes in only a few cell types. We also identify differences between widely used wild-type strains, compare phenotyping of gain- versus loss-of-function mutants and characterize deletions of topological associating domain boundaries. Notably, some changes are shared among mutants, suggesting that developmental pleiotropy might be 'decomposable' through further scaling of this approach. Overall, our findings show how single-cell profiling of whole embryos can enable the systematic molecular and cellular phenotypic characterization of mouse mutants with unprecedented breadth and resolution

Stress correlations of dislocations in a double-pileup configuration: A continuum dislocation density approach-Complas XII

Dislocation motion in the crystal lattice of materials is the basis for macroscopic plasticity. While continuum models for describing the role of dislocations in plasticity have existed for decades, only recently have the mathematical tools become available to describe ensembles of moving, oriented lines. These tools have allowed for the creation of a Continuum Dislocation Dynamics (CDD) theory describing a second-order dislocation density tensor, a higher order analog of the classical dislocation density tensor, and its evolution in time. In order to reduce the computational complexity of the theory, a simplified theory has also been developed, which more readily allows for a numerical implementation, useful for describing larger systems of dislocations. In order to construct a self-consistent implementation, several issues have to be resolved including calculation of the stress field of a system of dislocations, coarse graining, and boundary values. The present work d eals with the implementation including treatment of the near- and far-field stresses caused by the dislocation density tensor as well as boundary value considerations. The implementation is then applied to a few simple benchmark problems, notably the double pileup of dislocations in 1D. Applications to more general problems are considered, as well as comparisons with analytical solutions to classical dislocation problems. Focus is placed on problems where analytical solutions as well as simulations of discrete dislocations are known which act, along with experimental results, as the basis of comparison to determine the validity of the results

A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation

Establishing causal links between inherited polymorphisms and cancer risk is challenging. Here, we focus on the single-nucleotide polymorphism rs55705857, which confers a sixfold greater risk of isocitrate dehydrogenase ((IDH)-mutant low-grade glioma (LGG). We reveal that rs55705857 itself is the causal variant and is associated with molecular pathways that drive LGG. Mechanistically, we show that rs55705857 resides within a brain-specific enhancer, where the risk allele disrupts OCT2/4 binding, allowing increased interaction with the (Myc) promoter and increased (Myc) expression. Mutating the orthologous mouse rs55705857 locus accelerated tumor development in an Idh1(R132H)-driven LGG mouse model from 472 to 172 days and increased penetrance from 30% to 75%. Our work reveals mechanisms of the heritable predisposition to lethal glioma in ~40% of LGG patients